Mercurial > repos > bgruening > diamond

annotate macros.xml @ 9:f921014aba5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"
author iuc
date Sat, 27 Nov 2021 09:48:10 +0000
parents 54f751e413f4
children 1e3323a44643
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
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1 <macros>
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f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"
iuc
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2 <token name="@TOOL_VERSION@">2.0.8</token>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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4 <xml name="requirements">
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5 <requirements>
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f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"
iuc
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6 <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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7 </requirements>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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8 </xml>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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10 <xml name="stdio">
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11 <stdio>
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12 <regex match="Failed to allocate" source="stderr" level="fatal_oom" />
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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13 </stdio>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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14 </xml>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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16 <xml name="version_command">
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54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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17 <version_command>diamond version | cut -d" " -f 3</version_command>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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18 </xml>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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19
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64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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20 <xml name="output_type_macro">
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21 <conditional name="output">
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22 <param argument="--outfmt" type="select" label="Format of output file " help="">
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bgruening
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23 <option value="0">BLAST pairwise</option>
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24 <option value="5">BLAST XML</option>
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25 <option value="6">BLAST tabular</option>
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26 <option value="100">DAA</option>
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27 <option value="101">SAM</option>
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28 <option value="102">Taxonomic classification</option>
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29 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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30 <when value="0"/>
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54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
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31 <when value="5"/>
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64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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32 <when value="6">
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33 <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
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34 <option value="qseqid" selected="true">Query Seq - id</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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35 <option value="sseqid" selected="true">Subject Seq - id</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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36 <option value="sallseqid">All subject Seq - id(s)</option>
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37 <option value="qlen">Query sequence length</option>
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bgruening
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38 <option value="slen">Subject sequence length</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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39 <option value="pident" selected="true">Percentage of identical matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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40 <option value="length" selected="true">Alignment length</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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41 <option value="nident">Number of identical matches</option>
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bgruening
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42 <option value="mismatch" selected="true">Number of mismatches</option>
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bgruening
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43 <option value="positive">Number of positive - scoring matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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44 <option value="gapopen" selected="true">Number of gap openings</option>
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bgruening
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45 <option value="gaps">Total number of gaps</option>
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bgruening
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46 <option value="ppos">Percentage of positive - scoring matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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47 <option value="qstart" selected="true">Start of alignment in query</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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48 <option value="qend" selected="true">End of alignment in query</option>
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bgruening
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49 <option value="sstart" selected="true">Start of alignment in subject</option>
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bgruening
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50 <option value="send" selected="true">End of alignment in subject</option>
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bgruening
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51 <option value="qseq">Aligned part of query sequence</option>
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bgruening
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52 <option value="sseq">Aligned part of subject sequence</option>
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53 <option value="qseq_translated">Translation of the aligned part of query sequence</option>
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54 <option value="evalue" selected="true">Expect value</option>
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55 <option value="bitscore" selected="true">Bit score</option>
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56 <option value="score">Raw score</option>
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57 <option value="qframe">Query frame</option>
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58 <option value="btop">Blast traceback operations(BTOP)</option>
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59 <option value="scovhsp">Subject coverage per HSP</option>
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60 <option value="stitle">Subject Title</option>
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61 <option value="salltitles">All Subject Title(s)</option>
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62 <option value="qcovhsp">Query Coverage Per HSP</option>
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63 <option value="qtitle">Query title</option>
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62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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64 <option value="full_qseq">Query sequence</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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65 <option value="full_sseq">Subject sequence</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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66 <option value="qqual">Query quality values for the aligned part of the query</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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67 <option value="full_qqual">Query quality values</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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68 <option value="qstrand">Query strand</option>
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69 <option value="cigar">Cigar</option>
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70 <yield/>
6
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71 </param>
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f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"
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72 <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
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73 </when>
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74 <when value="100">
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75 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
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76 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
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77 </when>
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54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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78 <when value="101">
6
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79 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
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80 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
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81 </when>
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82 <when value="102"/>
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83 </conditional>
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84 </xml>
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85
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bgruening
parents: 1
diff changeset
86 <xml name="hit_filter_macro">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
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87 <conditional name="hit_filter">
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parents: 1
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88 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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89 <option value="max">Maximum number of target sequences</option>
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90 <option value="top">Percentage of top alignment score</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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91 </param>
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92 <when value="max">
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93 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found." />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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parents: 1
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94 </when>
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parents: 1
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95 <when value="top">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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96 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all align-
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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97 ments whose score is at most 10% lower than the best alignment score for a query." />
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98 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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99 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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100 </xml>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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101
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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102 <xml name="block_size_low_sens">
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103 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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104 </xml>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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105
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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106 <xml name="block_size_hi_sens">
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107 <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
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108 </xml>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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109
1
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110 <xml name="citations">
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111 <citations>
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112 <citation type="doi">10.1038/nmeth.3176</citation>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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113 </citations>
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114 </xml>
6
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115
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116
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117 <xml name="output_macro">
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118 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}">
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119 <filter>output["outfmt"] == "0"</filter>
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120 </data>
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121 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">
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122 <filter>output["outfmt"] == "5"</filter>
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123 </data>
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124 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
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125 <filter>output["outfmt"] == "6"</filter>
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126 </data>
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127 <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
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128 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa">
6
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129 <filter>output["outfmt"] == "100"</filter>
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130 </data>
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131 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
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132 <filter>output["outfmt"] == "101"</filter>
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133 </data>
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134 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}">
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135 <filter>output["outfmt"] == "102"</filter>
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136 </data>
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137 </xml>
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138
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139 <token name="@OUTPUT_ARGS@">
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140 #if $output.outfmt == "0"
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141 --outfmt '0'
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142 --out '$blast_pairw'
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143 #else if $output.outfmt == "5"
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144 --outfmt '5'
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145 --out '$blast_xml'
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146 #else if $output.outfmt == "6"
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147 --outfmt '6' #echo ' '.join(str($output.fields).split(','))
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148 --out '$blast_tabular'
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149 --unal $output.unal
6
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150 #else if $output.outfmt == "100"
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151 --outfmt '100'
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152 $output.salltitles
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153 $output.sallseqid
6
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154 --out output.daa
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155 #else if $output.outfmt == "101"
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156 --outfmt '101'
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157 $output.salltitles
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158 $output.sallseqid
6
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159 --out '$sam_output'
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160 #else if $output.outfmt == "102"
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161 --outfmt '102'
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162 --out '$tax_output'
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163 #end if
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164 </token>
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165
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166 <token name="@HITFILTER_ARGS@">
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167 #if str($hit_filter.hit_filter_select) == 'max':
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168 --max-target-seqs '$hit_filter.max_target_seqs'
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169 #else:
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170 --top '$hit_filter.top'
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171 #end if
6
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172 </token>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
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